lib/CXGN/Cview/Map/SGN/Genetic.pm

   1 package CXGN::Cview::Map::SGN::Genetic;
   2
   3 =head1 NAME
   4
   5 CXGN::Cview::Map::SGN::Genetic - a class implementing a genetic map
   6
   7 =head1 DESCRIPTION
   8
   9 This class implements a genetic map populated from the SGN database. This class inherits from L<CXGN::Cview::Map>.
  10
  11 Note: the common name (available through get_common_name()) for the map organism is now taken through the following join: sgn.accession -> public.organism -> sgn.organismgroup_member ->sgn.organism_group (July 2010).
  12
  13 =head1 AUTHOR(S)
  14
  15 Lukas Mueller <lam87@cornell.edu>
  16
  17 =head1 FUNCTIONS
  18
  19 This class implements the following functions (for more information, see L<CXGN::Cview::Map>):
  20
  21 =cut
  22
  23 use strict;
  24 use warnings;
  25
  26 use CXGN::Cview::Legend::Genetic;
  27 use CXGN::Cview::Map;
  28 use CXGN::Cview::Map::Tools;
  29
  30 use base qw | CXGN::Cview::Map |;
  31
  32 =head2 function new
  33
  34   Synopsis:     my $genetic = CXGN::Cview::Map::SGN::Genetic->
  35                   new( $dbh, $map_version_id);
  36   Arguments:    (1) a database handle, preferably generated with
  37                     CXGN::DB::Connection
  38                 (2) the map version id for the desired map.
  39   Returns:      a Genetic map object
  40   Side effects: accesses the database
  41   Description:
  42
  43 =cut
  44
  45 sub new {
  46     my $class = shift;
  47     my $dbh = shift;
  48     my $map_version_id = shift;
  49
  50     my $self = $class->SUPER::new($dbh);
  51     $self->set_id($map_version_id);
  52     $self->fetch();
  53
  54     # set some defaults
  55     $self->set_preferred_chromosome_width(20);
  56
  57     # fetch the chromosome lengths
  58     #
  59     my $query = "SELECT lg_name, max(position) FROM sgn.linkage_group JOIN sgn.marker_location USING(lg_id) WHERE linkage_group.map_version_id=? GROUP BY lg_name, lg_order ORDER BY lg_order";
  60     my $sth = $self->get_dbh()->prepare($query);
  61     $sth->execute($self->get_id());
  62     my @chromosome_lengths = ();
  63     while (my ($lg_name, $length) = $sth->fetchrow_array()) {
  64         push @chromosome_lengths, $length;
  65     }
  66     $self->set_chromosome_lengths(@chromosome_lengths);
  67
  68     if ($self->get_chromosome_count() == 0) { return undef; }
  69
  70     my $legend = CXGN::Cview::Legend::Genetic->new($self);
  71 #    $legend->set_mode("marker_types");
  72     $self->set_legend($legend);
  73
  74     return $self;
  75 }
  76
  77 sub fetch {
  78     my $self = shift;
  79
  80     # get the map metadata
  81     #
  82     my $query = "SELECT map_version_id, map_type, short_name, long_name, abstract, public.organism.common_name, organismgroup.name FROM sgn.map JOIN sgn.map_version using(map_id) LEFT JOIN sgn.accession on(parent_1=accession.accession_id) LEFT JOIN public.organism on (public.organism.organism_id=accession.chado_organism_id) LEFT JOIN sgn.organismgroup_member on (public.organism.organism_id=organismgroup_member.organism_id) join sgn.organismgroup using(organismgroup_id)  WHERE map_version_id=?";
  83     my $sth = $self->get_dbh()->prepare($query);
  84     $sth->execute($self->get_id());
  85     my ($map_version_id, $map_type, $short_name, $long_name, $abstract, $organism_name, $common_name) = $sth->fetchrow_array();
  86     $self->set_id($map_version_id);
  87     $self->set_type($map_type);
  88     $self->set_short_name($short_name);
  89     $self->set_long_name($long_name);
  90     $self->set_abstract($abstract);
  91     $self->set_organism($organism_name);
  92     $self->set_common_name($common_name);
  93     $self->set_units("cM");
  94
  95     # get information about associated linkage_groups
  96     #
  97     my $chr_name_q = "SELECT distinct(linkage_group.lg_name), lg_order FROM sgn.linkage_group WHERE map_version_id=? ORDER BY lg_order";
  98     my $chr_name_h = $self->get_dbh()->prepare($chr_name_q);
  99     $chr_name_h->execute($self->get_id());
 100     my @names = ();
 101     while (my ($lg_name) = $chr_name_h->fetchrow_array()) {
 102         push @names, $lg_name;
 103     }
 104     $self->set_chromosome_names(@names);
 105     $self->set_chromosome_count(scalar(@names));
 106     $self->set_preferred_chromosome_width(20);
 107
 108     # get the location of the centromeres
 109     #
 110     my $centromere_q = "SELECT lg_name, min(position) as north_centromere, max(position) as south_centromere FROM linkage_group left join marker_location on (north_location_id=location_id or south_location_id=location_id) where linkage_group.map_version_id=? group by linkage_group.lg_id, linkage_group.map_version_id, lg_order, lg_name order by lg_order";
 111     my $centromere_h = $self->get_dbh()->prepare($centromere_q);
 112     $centromere_h->execute($self->get_id());
 113     while (my ($lg_name, $north, $south) = $centromere_h->fetchrow_array()) {
 114         $self->set_centromere($lg_name, $north, $south);
 115     }
 116
 117
 118 }
 119
 120 =head2 function get_chromosome
 121   Synopsis:     see L<CXGN::Cview::Map>
 122   Arguments:
 123   Returns:
 124   Side effects:
 125   Description:
 126
 127 =cut
 128
 129 sub get_chromosome {
 130     my $self = shift;
 131     my $chr_nr = shift;
 132 #    my $marker_confidence_cutoff = shift; # the confidence cutoff. 3=frame 2=coseg 1=interval LOD=2 0=interval
 133
 134 #    if (!$marker_confidence_cutoff) { $marker_confidence_cutoff=-1; }
 135
 136     my $chromosome = CXGN::Cview::Chromosome->new();
 137     $chromosome->set_name($chr_nr);
 138     $chromosome->set_caption($chr_nr);
 139
 140     my %seq_bac = ();
 141
 142     my $physical = 'physical';
 143
 144     if ($self->get_id() == CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id())) {
 145
 146         # get the sequenced BACs
 147         #
 148         my $Sequenced_BAC_query =
 149         "
 150             SELECT
 151                 distinct $physical.bac_marker_matches.bac_id,
 152                 $physical.bac_marker_matches.cornell_clone_name,
 153                 $physical.bac_marker_matches.marker_id,
 154                 $physical.bac_marker_matches.position
 155             FROM
 156                 $physical.bac_marker_matches
 157                 LEFT JOIN sgn.linkage_group USING (lg_id)
 158                 LEFT JOIN sgn_people.bac_status USING (bac_id)
 159             WHERE
 160                 sgn.linkage_group.lg_name=?
 161                 AND sgn_people.bac_status.status='complete'
 162         ";
 163         my $sth2 = $self->get_dbh->prepare($Sequenced_BAC_query);
 164         $sth2->execute($chr_nr);
 165         while (my ($bac_id, $name, $marker_id, $offset)=$sth2->fetchrow_array()) {
 166 # print STDERR "Sequenced BAC for: $bac_id, $name, $marker_id, $offset...\n";
 167             $name = CXGN::Genomic::Clone->retrieve($bac_id)->clone_name();
 168
 169             my $m = CXGN::Cview::Marker::SequencedBAC->new($chromosome, $bac_id, $name, "", "", "", "", $offset);
 170             $m->get_label()->set_text_color(200,200,80);
 171             $m->get_label()->set_line_color(200,200,80);
 172             $seq_bac{$marker_id}=$m;
 173         }
 174     }
 175
 176     # get the "normal" markers
 177     #
 178     my $query =     "
 179         SELECT
 180             marker_experiment.marker_id,
 181             alias,
 182             mc_name,
 183             confidence_id,
 184             0,
 185             subscript,
 186             position,
 187             0
 188         FROM
 189             sgn.map_version
 190             inner join sgn.linkage_group using (map_version_id)
 191             inner join sgn.marker_location using (lg_id)
 192             inner join sgn.marker_experiment using (location_id)
 193             inner join sgn.marker_alias using (marker_id)
 194             inner join sgn.marker_confidence using (confidence_id)
 195             left join sgn.marker_collectible using (marker_id)
 196             left join sgn.marker_collection using (mc_id)
 197         WHERE
 198             map_version.map_version_id=?
 199             and lg_name=?
 200             and preferred='t'
 201          ORDER BY
 202             position,
 203             confidence_id desc
 204     ";
 205
 206     #print STDERR "MY ID: ".$self->get_id()." MY CHR NR: ".$chr_nr."\n";
 207
 208     my $sth =  $self->get_dbh -> prepare($query);
 209     $sth -> execute($self->get_id(), $chr_nr);
 210
 211     while (my ($marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, $loc_type) = $sth->fetchrow_array()) {
 212         #print STDERR "Marker Read: $marker_id\t$marker_name\t$marker_type\t$offset\n";
 213         my $m = CXGN::Cview::Marker -> new($chromosome, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, undef , $loc_type, 0);
 214         #print STDERR "dataadapter baccount = $bac_count!\n";
 215         if ($loc_type == 100) { $m -> set_frame_marker(); }
 216         $m -> set_url( $self->get_marker_link($m->get_id()));
 217         $self->set_marker_color($m, $self->get_legend()->get_mode());
 218
 219         #print STDERR "CURRENT MODE IS: ".$self->get_legend()->get_mode()."\n";
 220         $chromosome->add_marker($m);
 221
 222         if (exists($seq_bac{$marker_id})) {
 223             #print STDERR "Adding Sequenced BAC [".($seq_bac{$marker_id}->get_name())."] to map...[$marker_id]\n";
 224             $chromosome->add_marker($seq_bac{$marker_id});
 225         }
 226     }
 227
 228
 229     foreach my $mi ($self->get_map_items()) {
 230
 231         my ($chr, $offset, $name) = split /\s+/, $mi;
 232
 233
 234         if (!$chr || !$offset || !$name) { next; }
 235
 236         if ($chr ne $chr_nr) { next; }
 237
 238         my $m = CXGN::Cview::Marker->new($chromosome);
 239
 240         $m->get_label()->set_label_text($name);
 241         $m->set_offset($offset);
 242         $m->get_label()->set_hilited(1);
 243         $m->show_label();
 244         $m->get_label()->set_url('');
 245         $m->set_marker_name($name); # needed for proper marker ordering in the chromosome
 246         $chromosome->add_marker($m);
 247
 248
 249     }
 250
 251     $chromosome->sort_markers();
 252
 253     $chromosome -> _calculate_chromosome_length();
 254
 255     return $chromosome;
 256 }
 257
 258
 259 =head2 function get_chromosome_section
 260
 261   Synopsis:     my $chr_section = $map->get_chromosome_section(5, 120, 180);
 262   Arguments:    linkage group number, start offset, end offset
 263   Returns:
 264   Side effects:
 265   Description:
 266
 267 =cut
 268
 269 sub get_chromosome_section {
 270     my $self = shift;
 271     my $chr_nr = shift;     # the chromosome number
 272     my $start = shift;      # the start of the section in cM
 273     my $end = shift;        # the end of the section in cM
 274
 275     my $chromosome = CXGN::Cview::Chromosome->new();
 276
 277     # main query to get the marker data, including the BACs that
 278     # are associated with this marker -- needs to be refactored to
 279     # work with the materialized views for speed improvements.
 280     #
 281     my $query =
 282     "
 283         SELECT
 284             marker_experiment.marker_id,
 285             alias,
 286             mc_name,
 287             confidence_id,
 288             0,
 289             subscript,
 290             position,
 291             0,
 292             min(physical.probe_markers.overgo_probe_id),
 293             count(distinct(physical.overgo_associations.bac_id)),
 294             max(physical.oa_plausibility.plausible)
 295         FROM
 296             map_version
 297             inner join linkage_group using (map_version_id)
 298             inner join marker_location using (lg_id)
 299             inner join marker_experiment using (location_id)
 300             inner join marker_alias using (marker_id)
 301             inner join marker_confidence using (confidence_id)
 302             left join marker_collectible using (marker_id)
 303             left join marker_collection using (mc_id)
 304             LEFT JOIN physical.probe_markers ON (marker_experiment.marker_id=physical.probe_markers.marker_id)
 305             LEFT JOIN physical.overgo_associations USING (overgo_probe_id)
 306             LEFT JOIN physical.oa_plausibility USING (overgo_assoc_id)
 307         WHERE
 308             map_version.map_version_id=?
 309             and lg_name=?
 310             and preferred='t'
 311             -- and current_version='t'
 312             AND position >= ?
 313             AND position <= ?
 314         GROUP BY
 315             marker_experiment.marker_id,
 316             alias,
 317             mc_name,
 318             confidence_id,
 319             subscript,
 320             position
 321         ORDER BY
 322             position,
 323             confidence_id desc,
 324             max(physical.oa_plausibility.plausible),
 325             max(physical.probe_markers.overgo_probe_id)
 326     ";
 327
 328
 329     my $sth =  $self->get_dbh()-> prepare($query);
 330 #    print STDERR "START/END: $start/$end\n";
 331     $sth -> execute($self->get_id(), $chr_nr, $start, $end);
 332
 333     # for each marker, look if there is a associated fully sequenced BAC, and add that
 334     # as a marker of type Sequenced_BAC to the map at the right location
 335     #
 336     my $bac_status_q =
 337     "
 338         SELECT
 339             cornell_clone_name,
 340             bac_id
 341         FROM
 342             physical.bac_marker_matches
 343             JOIN sgn_people.bac_status using (bac_id)
 344         WHERE
 345             physical.bac_marker_matches.marker_id=?
 346             AND sgn_people.bac_status.status='complete'
 347     ";
 348
 349     my $bac_status_h = $self->get_dbh()->prepare($bac_status_q);
 350     my $seq_bac;
 351
 352     while (my ($marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, $loc_type, $overgo, $bac_count, $plausible, $status, $bac_name, $bac_id) = $sth->fetchrow_array()) {
 353         #print STDERR "Marker Read: $marker_id\t$marker_name\t$marker_type\toffset: $offset\tovergo: $overgo\tbac_count: $bac_count\tplausible: $plausible\n";
 354         my $seq_bac=undef;
 355         my $seq_bac_name="";
 356         my $seq_bac_id="";
 357         if (!$plausible || $plausible == 0)  { $bac_count = 0; }
 358         my $m = CXGN::Cview::Marker -> new($chromosome, $marker_id, $marker_name, $marker_type, $confidence, $order_in_loc, $location_subscript, $offset, , $loc_type, 0, $overgo, $bac_count);
 359         $m->set_url($self->get_marker_link($m->get_id()));
 360         $self->set_marker_color($m, $self->get_legend()->get_mode());
 361         #print STDERR "dataadapter baccount = $bac_count!\n";
 362         if ($loc_type == 100) { $m -> set_frame_marker(); }
 363
 364         # only add the sequenced BAC information to the F2-2000.
 365         #
 366         if ($self->get_id() == CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id())) {
 367
 368             $bac_status_h->execute($marker_id);
 369             ($seq_bac_name, $seq_bac_id) = $bac_status_h->fetchrow_array();
 370
 371             # change the name to look more standard
 372             #
 373             if ($seq_bac_name) {
 374                  if ($seq_bac_name =~ m/(\d+)([A-Z])(\d+)/i) {
 375                     $seq_bac_name = sprintf ("%3s%04d%1s%02d", "HBa",$1,$2,$3);
 376                 }
 377                 $seq_bac = CXGN::Cview::Marker::SequencedBAC->new($chromosome, $seq_bac_id, $seq_bac_name, "", "", "", "", $offset);
 378             }
 379         }
 380
 381         # add the marker $m to the chromosome
 382         #
 383         $chromosome->add_marker($m);
 384
 385         if ($m->has_overgo()) {
 386                 $m->set_mark_color(100, 100, 100); # draw a gray circle for overgos
 387                 $m->set_show_mark(1);
 388                 $m->set_mark_link( "/tools/seedbac/sbfinder.pl?marker=".$m->get_marker_name()  );
 389             }
 390         #print STDERR "# BACS: ".($m2[$i]->has_bacs())."\n";
 391         if ($m->has_bacs()) {
 392             $m->set_mark_color(180, 0, 0); # draw a red circle for associated bacs
 393             $m->set_show_mark(1);
 394             $m->set_mark_link("/tools/seedbac/sbfinder.pl?marker=".$m->get_marker_name());
 395         }
 396         if (!$m->is_visible()) {
 397             $m->set_show_mark(0);
 398         }
 399
 400         # add the sequenced BAC to the chromosome
 401         # -url link needs to be changed
 402         # -add a confidence level of 3 so that it is always displayed.
 403         #
 404         if ($seq_bac) {
 405             $seq_bac->set_confidence(3);
 406             $seq_bac->set_url("/maps/physical/clone_info.pl?id=$seq_bac_id");
 407             $chromosome->add_marker($seq_bac);
 408         }
 409     }
 410     $chromosome->set_section($start, $end);
 411     $chromosome -> _calculate_chromosome_length();
 412
 413
 414
 415     return $chromosome;
 416 }
 417
 418 =head2 function get_overview_chromosome
 419
 420   Synopsis:
 421   Arguments:
 422   Returns:
 423   Side effects:
 424   Description:
 425
 426 =cut
 427
 428 sub get_overview_chromosome {
 429     my $self = shift;
 430     my $chr_nr = shift;
 431     my $chr = $self->get_chromosome($chr_nr);
 432     $chr->set_width( $self->get_preferred_chromosome_width()/2 );
 433     foreach my $m ($chr->get_markers()) {
 434         $m->hide_label();
 435         $m->hide_mark();
 436     }
 437     return $chr;
 438 }
 439
 440 =head2 get_chromosome_connections()
 441
 442  Usage:        @list = $map->get_chromosome_connections($lg_name)
 443  Args:         a linkage group name from the current map
 444  Returns:      a list of hashrefs, containing 4 keys
 445                map_version_id, lg_name, marker_count, short_name
 446                and the corresponding values
 447  Side Effects: the information will be used to populate the
 448                drop down menu in the comparative viewer.
 449  Example:
 450
 451 =cut
 452
 453 sub get_chromosome_connections {
 454     my $self = shift;
 455     my $chr_nr = shift;
 456
 457     my $query =
 458         "
 459         SELECT
 460             c_map_version.map_version_id,
 461             c_map.short_name,
 462             c_linkage_group.lg_name,
 463             count(distinct(marker.marker_id)) as marker_count
 464         from
 465             marker
 466             join marker_experiment using(marker_id)
 467             join marker_location using (location_id)
 468             join linkage_group on (marker_location.lg_id=linkage_group.lg_id)
 469             join map_version on (linkage_group.map_version_id=map_version.map_version_id)
 470
 471             join marker_experiment as c_marker_experiment on
 472                  (marker.marker_id=c_marker_experiment.marker_id)
 473             join marker_location as c_marker_location on
 474                  (c_marker_experiment.location_id=c_marker_location.location_id)
 475             join linkage_group as c_linkage_group on (c_marker_location.lg_id=c_linkage_group.lg_id)
 476             join map_version as c_map_version on
 477                  (c_linkage_group.map_version_id=c_map_version.map_version_id)
 478             join map as c_map on (c_map.map_id=c_map_version.map_id)
 479         where
 480             map_version.map_version_id=?
 481             and linkage_group.lg_name=?
 482             and c_map_version.map_version_id !=map_version.map_version_id
 483             and c_map_version.current_version='t'
 484         group by
 485             c_map_version.map_version_id,
 486             c_linkage_group.lg_name,
 487             c_map.short_name
 488         order by
 489             marker_count desc
 490     ";
 491
 492     my $sth = $self->get_dbh() -> prepare($query);
 493     $sth -> execute($self->get_id(), $chr_nr);
 494     my @chr_list = ();
 495
 496     #print STDERR "***************** Done with query..\n";
 497     while (my $hashref = $sth->fetchrow_hashref()) {
 498         #print STDERR "READING----> $hashref->{map_version_id} $hashref->{lg_name} $hashref->{marker_count}\n";
 499         push @chr_list, $hashref;
 500
 501     }
 502
 503     # hard code some connections to agp and fish maps.
 504     #
 505     my $tomato_version_id = CXGN::Cview::Map::Tools::find_current_version($self->get_dbh(), CXGN::Cview::Map::Tools::current_tomato_map_id());
 506     ###print STDERR $self->get_id()." VERSUS $tomato_version_id\n\n";
 507
 508     if ($self->get_id() == $tomato_version_id) {
 509
 510         ##print STDERR "***** Map ".$self->get_id(). " pushing agp and fish map!\n\n";
 511         push @chr_list, { map_version_id => "agp",
 512                           short_name => "Tomato AGP map",
 513                           lg_name => $chr_nr,
 514                           marker_count => "?"
 515                           };
 516         push @chr_list, { map_version_id => 25,
 517                           short_name => "FISH map",
 518                           lg_name => $chr_nr,
 519                           marker_count => "?"
 520                           };
 521     }
 522     else {
 523         warn $self->get_id()." has no other associated maps...\n\n";
 524     }
 525
 526     return @chr_list;
 527 }
 528
 529 =head2 function has_linkage_group
 530
 531   Synopsis:
 532   Arguments:
 533   Returns:
 534   Side effects:
 535   Description:
 536
 537 =cut
 538
 539 sub has_linkage_group {
 540     my $self = shift;
 541     my $candidate = shift;
 542     foreach my $lg ($self->get_chromosome_names()) {
 543         if ($lg eq $candidate) {
 544             return 1;
 545         }
 546     }
 547     return 0;
 548 }
 549
 550 =head2 function get_marker_count
 551
 552 accesses the database to count the marker on the given map/chromosome.
 553
 554 =cut
 555
 556 sub get_marker_count {
 557     my $self =shift;
 558     my $chr_name = shift;
 559     my $query = "SELECT count(distinct(location_id)) FROM sgn.map_version JOIN marker_location using (map_version_id)
 560                             JOIN linkage_group using (lg_id)
 561                       WHERE linkage_group.lg_name=? and map_version.map_version_id=?";
 562     my $sth = $self->get_dbh()->prepare($query);
 563     $sth->execute($chr_name, $self->get_id());
 564     my ($count) = $sth->fetchrow_array();
 565     return $count;
 566
 567 }
 568
 569 sub get_map_stats {
 570     my $self = shift;
 571     my $query =
 572     "
 573         select
 574             mc_name,
 575             count(distinct(marker.marker_id))
 576         from
 577             marker join marker_collectible using (marker_id)
 578             join marker_collection using(mc_id)
 579             join marker_experiment on (marker.marker_id=marker_experiment.marker_id)
 580             join marker_location on (marker_experiment.location_id=marker_location.location_id)
 581         where
 582             marker_location.map_version_id=?
 583         group by
 584             mc_name
 585     ";
 586
 587     my $total_count = 0;
 588
 589     my $s = "<table summary=\"\"><tr><td>&nbsp;</td><td>\# markers</td></tr>";
 590     my $sth = $self->get_dbh() -> prepare($query);
 591     $sth -> execute($self->get_id());
 592
 593     my $map_name = $self->get_short_name();
 594     $map_name =~ s/ /\+/g;
 595
 596     while (my ($type, $count)= $sth->fetchrow_array()) {
 597         $s .="<tr><td>$type</td><td align=\"right\"><a href=\"/search/markers/markersearch.pl?types=$type&amp;maps=$map_name\">$count</a></td></tr>";
 598         $total_count += $count;
 599
 600
 601     }
 602     $s .= "<tr><td>&nbsp;</td><td>&nbsp;</td></tr>\n";
 603     $s .= "<tr><td><b>Total</b>: </td><td align=\"right\"><a href=\"/search/markers/markersearch.pl?maps=$map_name\"><b>$total_count</b></a></td></tr>";
 604     $s .= "</table>";
 605
 606     my $protocol_q = "SELECT distinct(marker_experiment.protocol), count(distinct(marker_experiment.marker_experiment_id))
 607                         FROM marker
 608                         JOIN marker_experiment using (marker_id)
 609                         JOIN marker_location using (location_id)
 610                         JOIN linkage_group using (map_version_id)
 611                        WHERE map_version_id=?
 612                        GROUP BY marker_experiment.protocol";
 613     my $pqh = $self->get_dbh()->prepare($protocol_q);
 614     $pqh ->execute($self->get_id());
 615
 616     my $total_protocols = 0;
 617     $s.= qq { <br /><br /><table><tr><td colspan="2"><b>Protocols:</b></td></tr> };
 618     $s.= qq { <tr><td>&nbsp;</td><td>&nbsp;</td></tr> };
 619     $s.= qq { <tr><td>&nbsp;</td><td>\# markers</td></tr> };
 620     while (my ($protocol, $count) = $pqh->fetchrow_array()) {
 621         $s.= qq { <tr><td>$protocol</td><td align="right">$count</td></tr> };
 622         $total_protocols += $count;
 623     }
 624     $s .= qq { <tr><td colspan="2">&nbsp;</td></tr> };
 625     $s .= qq { <tr><td><b>Total:</b></td><td align="right"><b>$total_protocols</b></td></tr> };
 626     $s .= "</table>";
 627
 628     return $s;
 629 }
 630
 631
 632
 633 =head2 function has_IL
 634
 635   Synopsis:
 636   Arguments:
 637   Returns:
 638   Side effects:
 639   Description:
 640
 641 =cut
 642
 643 sub has_IL {
 644     my $self =shift;
 645
 646     if ($self->get_short_name()=~/1992|2000/) {
 647         #print STDERR "Map ".$self->get_short_name()." has an associated IL map.\n";
 648         return 1;
 649     }
 650     #print STDERR "Map ".$self->get_short_name()." does not have an associated IL map.\n";
 651     return 0;
 652 }
 653
 654 =head2 function has_physical
 655
 656   Synopsis:
 657   Arguments:
 658   Returns:
 659   Side effects:
 660   Description:
 661
 662 =cut
 663
 664 sub has_physical {
 665     my $self = shift;
 666     if ($self->get_short_name()=~/2000/) {
 667         return 1;
 668     }
 669     return 0;
 670 }
 671
 672 =head2 function can_zoom
 673
 674 Whether this map support zooming in. These ones do.
 675
 676 =cut
 677
 678 sub can_zoom {
 679     return 1;
 680 }
 681
 682 =head2 function get_marker_link
 683
 684   Synopsis:
 685   Arguments:
 686   Returns:
 687   Side effects:
 688   Description:
 689
 690 =cut
 691
 692 sub get_marker_link {
 693     my $self =shift;
 694     my $id = shift;
 695     return "/search/markers/markerinfo.pl?marker_id=$id";
 696 }
 697
 698
 699 =head2 function set_marker_color()
 700
 701   Synopsis:
 702   Parameters:   marker object [CXGN::Cview::Marker], color model [string]
 703   Returns:      nothing
 704   Side effects: sets the marker color according to the supplied marker color model
 705                 the color model is a string from the list:
 706                 "marker_types", "confidence"
 707   Status:       implemented
 708   Example:
 709   Note:         this function was moved to Utils from ChromosomeViewer, such that
 710                 it is available for other scripts, such as view_maps.pl
 711
 712 =cut
 713
 714 sub set_marker_color {
 715     my $self = shift;
 716     my $m = shift;
 717     my $color_model = shift || '';
 718
 719     if ($color_model eq "marker_types") {
 720         if ($m->get_marker_type() =~ /RFLP/i) {
 721             $m->set_color(255, 0, 0);
 722             $m->set_label_line_color(255, 0,0);
 723             $m->set_text_color(255,0,0);
 724         }
 725         elsif ($m->get_marker_type() =~ /SSR/i) {
 726             $m->set_color(0, 255, 0);
 727             $m->set_label_line_color(0, 255,0);
 728             $m->set_text_color(0,255,0);
 729         }
 730         elsif ($m->get_marker_type() =~ /CAPS/i) {
 731             $m->set_color(0, 0, 255);
 732             $m->set_label_line_color(0, 0,255);
 733             $m->set_text_color(0,0,255);
 734         }
 735         elsif ($m->get_marker_type() =~ /COS/i) {
 736             $m->set_color(255,0 , 255);
 737             $m->set_label_line_color(255,0, 255);
 738             $m->set_text_color(255,0,255);
 739         }
 740         else {
 741             $m->set_color(0, 0, 0);
 742             $m->set_label_line_color(0, 0,0);
 743             $m->set_text_color(0,0,0);
 744         }
 745
 746     }
 747     else {
 748         my $c = $m -> get_confidence();
 749         if ($c==0) {
 750             $m->set_color(0,0,0);
 751             $m->set_label_line_color(0,0,0);
 752             $m->set_text_color(0,0,0);
 753         }
 754         if ($c==1) {
 755             $m->set_color(0,0,255);
 756             $m->set_label_line_color(0,0,255);
 757             $m->set_text_color(0,0,255);
 758
 759         }
 760         if ($c==2) {
 761             $m->set_color(0,255, 0);
 762             $m->set_label_line_color(0,255,0);
 763             $m->set_text_color(0,255,0);
 764         }
 765         if ($c==3) {
 766             $m->set_color(255, 0, 0);
 767             $m->set_label_line_color(255, 0,0);
 768             $m->set_text_color(255, 0,0);
 769         }
 770         if ($c==4) {
 771             $m->set_color(128, 128, 128);
 772             $m->set_label_line_color(128, 128, 128);
 773             $m->set_text_color(128, 128, 128);
 774         }
 775     }
 776 }
 777
 778 sub can_overlay {
 779     return 1;
 780 }
 781
 782
 783 1;